Okay do not read this if you do not want spoilers of the End of Time for Doctor Who:
These are my thoughts and opinions of The End of Time, along with all the 2009 special episodes.
It's times like this when I look at the plot and think of all that missed potential. Seriously, they knew this was coming, and they had in mind a really awesome idea for an ending, and then they just bland it up.
These specials they had... the 11th Doctor had some moments, as did the Waters of Mars, but if they REALLY wanted to have made the "most awesome send-off ending evar" TM then they really should have not allowed the ending of Season 4 to have been a bigger bang than this one, cause it was.The presence of the various companions was greatly enjoyable, the very real threat of the enemey was great.
However, so much of what happened there eclipsed this ending. Maybe there were production constraints that I'm not aware of, but they really should have played this plot out over ALL five specials. Just follow the five act arc, and you have a miniseries for the fifth season worthy of remembering (it worked for Torchwood).
In such a scope, there would have been really awesome opportunity for the involvement of all the additional companions, as well as tieing in all the plot lines together in a much neater fashion. Granted... maybe they're just setting things up for their exploration later in season 5 (I hope).
End of Season 4: Things that should have stayed - Doctor Donna (the whole metacrisis thing should not have produced a second Doctor just yet); in fact the whole "I'm going to not do my regeneration" could have caused the metacrisis more Directly, making the Doctor kind of more directly responsible for her creation. It might have even been nice to have somehow worked in Susan Foreman or the Doctor's Daughter into that - a whole bloodlines thing.
Things that should have been saved - The second dimension and Torchwood's involvement.
Therefore, we finish season 4 with the whole "Bad Wolf" premonition of realities breaking down.
Ie: the the whole attempt to destroy reality using characters that are already in the Time Lock (Davros) becomes the hook that allows the events of the time lord arc to rise.
11th Doctor (exposition): While the concepts of this show were quite good... I think it would have been more interesting if the 11th Doctor actually did make an appearance. The fact that he's meeting his future self is a great war to foreshadow the threat of time unravelling. It confronts the 10th with his imminent death, and is a great way to trigger his attempt into becoming Time Lord Victorious.
Waters of Mars (escalation): Seriously, do we deed the Planet of the Dead? The only thing really relevant in that episode was the prophecy, which can happen in any episode. Instead this episode could have played much the way it did, with the rise of the Doctor's Dark side and then the Ood delivering the knocking prophecy at the end as a way of confirming his coming death (they did have the ability to see through time after all).
The Master Race (Climax): rather than a back story about the Master being reborn... it should have been an entire episode in itself. It's a story about immortality and defeating death.
So really, Captain Jack should have been captured as a subject of study in an attempt to create the waters of life, using the rift in Torchwood to start getting access to the Time Vortex. Torchwood suddenly becomes the centre of operations for the home base of the master race cult - it also provides easy access for WHY this immortality gate is there, and the experimentation to use it.
It would have also been a great way to toy around with the Doctor's own growing desire to not die, and his experimentatons with the waters of Life on his hand or somesuch that gave birth to the Doctor Clone. This is just part of his attempt to become Time Lord Victorious... he's being seduced by the Master in a similar pursuit for undeath. Of course, this just results in the rise of the Master Race (it should be made clear that the Master Race are still human, but just connected in a subserviant hive-like fashion to the Master's mind). (notice - no dark sith powers mentioned)
The Return (detente): Said events have now started breaking apart the barriers between realities, they also start triggering the memories of Donna, and Mr. Smith is able to prevent the change of Sarah Jane Smith... enter Doctor Donna, Rose Tyler and Sarah Jane Smith. Arguably three of the most significant female companions of the Doctor (who are still happy to play parts in the show). Through this show, the Doctor is now caught in a struggle of will with the Master, who both prove to be parts of the Galifrey Xanatos Gambit, that brings back Galifrey. It then becomes an interesting way to have the two Doctors back to back. It is Doctor Donna, - Rose Tyler, and Sarah who are there to redeem him from this path. A sign that what makes The Doctor different to other time lords is his companions, and his connection to humanity.
However, the Doctor Clone, is the foil... he shoots the Galifreyan president and assumes the mantle of the Time Lord Victorious. The Time Lords cause Earth to be changed into Galifrey (rather than knocked out of orbit) and enslave the master race via the Master's mind to set up Earth/Galifrey (with the rift in Cardith as their path into the vortex) as their flag ship ready to conquer the universe. They start using the collective consciousness of the people of earth to start causing them to ascend (as the Doctor sort of did at the end of Season 3). In order to boost the signal, they cause the frequency to touch onto the End of Time (where we know the Master is living as Doctor Yana). This creates a temporal bridge amplifying the signal.
The Fall (revelation): The Master is kept as a prisoner to ensure the enslavement of the master race for Galifrey. It then becomes apparent that things from the Time War are starting to leak through. There are now two teams... the Doctor is working with Sarah Jane Smith and Rose Tyler. They have to try to undo the Galifreyan masterplan.
Meanwhile, Doctor Donna and Captain Jack are ready to infiltrate Torchwood because there is something there that they can use (The 28 October 2006 Radio Times, in an image of the Torchwood Three headquarters, identified a piece of large coral on Captain Jack Harkness's desk as the beginnings of a TARDIS. John Barrowman, who plays Jack in Torchwood and Doctor Who confirmed that "Jack's growing a TARDIS... It's probably been there for 30 years. I suppose in 500 years he'll be able to begin the carving process".). The Doctor Donna uses her genius and some other trick to produce a fully formed TARDIS from this coral by accelerating its growth. They then use this TARDIS to try and block the rip in time/space so as to stop the Nightmare Child from entering.
So the Doctor Finally confronts the Master, they resolve their issues with the Master feeling betrayed for being a pawn. So what does he do? He reminds the Master that he's controlling 6 billion thoughts: they suddenly chant master master master, and lo, he started becoming this god-like being and attacks the Doctor Clone. The Master brings down the Doctor Victorious with a mind burn, flooding him with the sound of drums and overwhelming him (the knocking four times DOES kill one of him). What is demonstrated here again is its not the Doctor being clever, but the fact that he's so clever that he can get other people to do the work needed.
Now we have the Doctor condemning Galifrey back into the time war, an act he achieves with the help of Doctor Donna and the Master. It's a disastrous event - the Master is thrown into some unknown time/space, the Doctor Donna and Doctor are both lethally wounded by the event. He creates a bridge with Donna to give some of the regenerative energy to complete the meta-crisis and transforming her into a full time lord and maybe triggering one of her own regenerations (so that they don't need Catherine Tate all the time).
Now, the 10th Doctor does his final goodbyes. The parting scene with Rose is reminiscent of the Dalek beach one... They're standing at the rift in Torchwood Three, ready to send people back to the other side of the dimensional rifft. Here the 10th Doctor is getting ready to say goodbye to his gathered companions. It is here that the Doctor Donna, asked for the Doctor's sonic screw driver... pulls out a chip from it, and uses it to download his memories into the now empty husk of a clone.
In this scene, Donna has given the 10th Doctor a way of surviving beyond the imminent regeneration with Rose (albiet in a human form).